The use of metabolomics to dissect plant responses to abiotic stresses

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era

Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.

Born to revive: molecular and physiological mechanisms of double tolerance in a paleotropical and resurrection plant

Resurrection plants recover physiological functions after complete desiccation. Almost all of them are native to tropical warm environments. However, the Gesneriaceae include four genera, remnant of the past palaeotropical flora, which inhabit temperate mountains. One of these species is additionally freezing-tolerant: Ramonda myconi. We hypothesise that this species has been able to persist in a colder climate thanks to some resurrection-linked traits. To disentangle the physiological mechanisms underpinning multistress tolerance to desiccation and freezing, we conducted an exhaustive seasonal assessment of photosynthesis (gas exchange, limitations to partitioning, photochemistry and galactolipids) and primary metabolism (through metabolomics) in two natural populations at different elevations. R. myconi displayed low rates of photosynthesis, largely due to mesophyll limitation. However, plants were photosynthetically active throughout the year, excluding a reversible desiccation period. Common responses to desiccation and low temperature involved chloroplast protection: enhanced thermal energy dissipation, higher carotenoid to Chl ratio and de-epoxidation of the xanthophyll cycle. As specific responses, antioxidants and secondary metabolic routes rose upon desiccation, while putrescine, proline and a variety of sugars rose in winter. The data suggest conserved mechanisms to cope with photo-oxidation during desiccation and cold events, while additional metabolic mechanisms may have evolved as specific adaptations to cold during recent glaciations.

Metabolome Profiling Supports the Key Role of the Spike in Wheat Yield Performance

Although the relevance of spike bracts in stress acclimation and contribution to wheat yield was recently revealed, the metabolome of this organ and its response to water stress is still unknown. The metabolite profiles of flag leaves, glumes and lemmas were characterized under contrasting field water regimes in five durum wheat cultivars. Water conditions during growth were characterized through spectral vegetation indices, canopy temperature and isotope composition. Spike bracts exhibited better coordination of carbon and nitrogen metabolisms than the flag leaves in terms of photorespiration, nitrogen assimilation and respiration paths. This coordination facilitated an accumulation of organic and amino acids in spike bracts, especially under water stress. The metabolomic response to water stress also involved an accumulation of antioxidant and drought tolerance related sugars, particularly in the spikes. Furthermore, certain cell wall, respiratory and protective metabolites were associated with genotypic outperformance and yield stability. In addition, grain yield was strongly predicted by leaf and spike bracts metabolomes independently. This study supports the role of the spike as a key organ during wheat grain filling, particularly under stress conditions and provides relevant information to explore new ways to improve wheat productivity including potential biomarkers for yield prediction.

Alteration of metabolic profiles in Lemna paucicostata culture and enhanced production of GABA and ferulic acid by ethephon treatment

Lemna species have been used in the food, feed, and pharmaceutical industries, as they are inexpensive sources of proteins, starches, and fatty acids. In this study, we treated L. paucicostata with different concentrations (0.05, 0.1, 0.2, 0.5, or 1 mM) of ethephon. The total dry weight decreased in all ethephon-treated groups compared to the control group. We also investigated the alteration of metabolic profiles induced by ethephon treatment by using gas chromatography-mass spectrometry. This analysis identified 48 metabolites, and the relative levels of most of alcohols, amino acids, fatty acids, and phenols increased by the ethephon treatment, whereas levels of organic acids and sugars decreased. Among these, the highest production of γ-aminobutyric acid (GABA, 5.041 ± 1.373 mg/L) and ferulic acid (0.640 ± 0.071 mg/L) was observed in the 0.5 mM and the 0.2 mM ethephon treatment groups, respectively. These results could be useful for large-scale culture of L. paucicostata with enhanced GABA and ferulic acid content for utilization in the food, feed, cosmetic, and pharmaceutical industries.

UV-B Radiation Largely Promoted the Transformation of Primary Metabolites to Phenols in Astragalus mongholicus Seedlings

: Ultraviolet-B (UV-B) radiation (280-320 nm) may induce photobiological stress in plants, activate the plant defense system, and induce changes of metabolites. In our previous work, we found that between the two Astragalus varieties prescribed by the Chinese Pharmacopoeia, Astragalus mongholicus has better tolerance to UV-B. Thus, it is necessary to study the metabolic strategy of Astragalus under UV-B radiation further. In the present study, we used untargeted gas chromatography-mass spectrometry (GC-MS) and targeted liquid chromatography-mass spectrometry (LC-MS techniques) to investigate the profiles of primary and secondary metabolic. The profiles revealed the metabolic response of Astragalus to UV-B radiation. We then used real-time polymerase chain reaction (RT-PCR) to obtain the transcription level of relevant genes under UV-B radiation (UV-B supplemented in the field, λmax = 313 nm, 30 W, lamp-leaf distance = 60 cm, 40 min·day-1), which annotated the responsive mechanism of phenolic metabolism in roots. Our results indicated that supplemental UV-B radiation induced a stronger shift from carbon assimilation to carbon accumulation. The flux through the phenylpropanoids pathway increased due to the mobilization of carbon reserves. The response of metabolism was observed to be significantly tissue-specific upon the UV-B radiation treatment. Among phenolic compounds, C6C1 carbon compounds (phenolic acids in leaves) and C6C3C6 carbon compounds (flavones in leaves and isoflavones in roots) increased at the expense of C6C3 carbon compounds. Verification experiments show that the response of phenolics in roots to UV-B is activated by upregulation of relevant genes rather than phenylalanine. Overall, this study reveals the tissues-specific alteration and mechanism of primary and secondary metabolic strategy in response to UV-B radiation.

Combined transcriptomic and metabolomic analyses uncover rearranged gene expression and metabolite metabolism in tobacco during cold acclimation

Cold temperatures often severely restrict the growth, distribution and productivity of plants. The freezing tolerance of plants from temperate climates can be improved by undergoing periods of cold acclimation (CA). Tobacco is an important economic plant and is sensitive to cold stress. However, the dynamic changes and regulatory mechanisms of gene expression and metabolic processes during CA remain largely unknown. In this study, we performed RNA sequencing and metabolomic profiling analyses to identify the genes and metabolites specifically expressed during CA. Our transcriptomic data revealed 6905 differentially expressed genes (DEGs) during CA. Functional annotation and enrichment analyses revealed that the DEGs were involved mainly in signal transduction, carbohydrate metabolism and phenylpropanoid biosynthesis. Moreover, a total of 35 significantly changed metabolites were identified during CA via an LC-MS platform. Many protective metabolites, such as amino acids, carbohydrates, tricarboxylic acid (TCA) cycle intermediates and phenylpropanoid-related substances, were identified during CA. The gene-metabolite network extensively outlined the biological processes associated with the utilization of sugars, activation of amino acid metabolism, TCA cycle and phenylpropanoid biosynthesis in tobacco under CA. The results of our present study provide a comprehensive view of signal transduction and regulation, gene expression and dynamic changes in metabolites during CA.

Phosphoproteomic and Metabolomic Analyses Reveal Sexually Differential Regulatory Mechanisms in Poplar to Nitrogen Deficiency

Nitrogen (N) is a key factor impacting physiological processes in plants. Many proteins have been investigated in male and female poplars under N limitation. However, little is known about sex differences in the protein modifications and metabolites that occur in poplar leaves in response to N deficiency. In this study, as compared to N-deficient males, N-deficient females suffered greater damage from N deficiency, including chloroplast disorganization and lipid peroxidation of cellular membranes. Male poplars had greater osmotic adjustment ability than did females, allowing greater accumulation of soluble metabolites. In addition, as compared to that in N-deficient males, glycolysis was less suppressed in N-deficient females for increased enzyme activities to consume excess energy. Moreover, we found that pronounced protein phosphorylation occurred during carbon metabolism and substance transport processes in both sexes of poplar under N-limiting conditions. Sex-specific metabolites mainly included intermediates in glycolysis, amino acids, and phenylpropanoid-derived metabolites. This study provides new molecular evidence that female poplars suffer greater negative effects from N deficiency than do male poplars.

Comparative metabolomics analysis reveals different metabolic responses to drought in tolerant and susceptible poplar species

Drought is one of the critical factors limiting tree growth and survival. Clarifying the adaptation to drought will facilitate the cultivation of drought-tolerant varieties. Metabolites, as direct signatures of biochemical functions, can uncover the biochemical pathways involved in drought responses. Here, we investigated the physiological and metabolic responses of drought-tolerant Populus simonii and drought-susceptible Populus deltoides cv. 'Danhong' to drought. Under drought conditions, P. simonii grew better and had a higher photosynthetic rate than P. deltoides cv. 'Danhong'. Global untargeted metabolite profiling was analyzed using gas chromatography time-of-flight mass spectrometry system. A total of 69 and 53 differentially accumulated metabolites were identified in drought-stressed P. simonii and P. deltoides cv. 'Danhong', respectively. The metabolisms of carbohydrate, amino acid, lipid and energy were involved in the drought responses common to both poplar species. The citric acid cycle was significantly inhibited to conserve energy, whereas multiple carbohydrates acting as osmolytes and osmoprotectants were induced to alleviate the adverse effects of drought stress. Unlike P. deltoides cv. 'Danhong', P. simonii underwent a specific metabolic reprogramming that enhanced non-enzymatic antioxidants, coordinated the cellular carbon/nitrogen balance and regulated wax biosynthesis. These results provide a reference for characterizing the mechanisms involved in poplar response to drought and for enhancing the drought tolerance of forest trees.

Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress

Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0-24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0-288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy.

Pharmaceuticals in treated wastewater induce a stress response in tomato plants

Pharmaceuticals remain in treated wastewater used to irrigate agricultural crops. Their effect on terrestrial plants is practically unknown. Here we tested whether these compounds can be considered as plant stress inducers. Several features characterize the general stress response in plants: production of reactive oxygen species acting as stress-response signals, MAPKs signaling cascade inducing expression of defense genes, heat shock proteins preventing protein denaturation and degradation, and amino acids playing signaling roles and involved in osmoregulation. Tomato seedlings bathing in a cocktail of pharmaceuticals (Carbamazepine, Valporic acid, Phenytoin, Diazepam, Lamotrigine) or in Carbamazepine alone, at different concentrations and during different time-periods, were used to study the patterns of stress-related markers. The accumulation of the stress-related biomarkers in leaf and root tissues pointed to a cumulative stress response, mobilizing the cell protection machinery to avoid metabolic modifications and to restore homeostasis. The described approach is suitable for the investigation of stress response of different crop plants to various contaminants present in treated wastewater.

Metabolomics to Characterize Adaptive and Signaling Responses in Legume Crops under Abiotic Stresses

Legume species are an important source of protein and other nutrients for human and livestock consumption, playing a central role in food security. Besides, legumes benefit agriculture because of their ability to establish symbiotic interactions with nitrogen-fixing bacteria, providing nitrogen for subsequent crops, which is very much appreciated for sustainable agricultural practices. However, like other food crops, legumes are highly vulnerable to climate variations, water stresses being the main constraint that negatively affects both crop quality and productivity. Because of this, the development of strategies to improve the tolerance of such cultivars against water stresses, as well as the study of effective approaches to monitor these improvements, have gained special attention during the last years. Among these strategies, metabolomics has been considered one of the most promising approaches for the detection and/or quantification of primary and secondary stress-responsive metabolites in abiotic stresses. In plant science, many research groups have been using metabolomics to evaluate the success of genetic modifications by the analysis of chemical markers that can be altered in breeding programs. In addition, metabolomics is a powerful tool for the evaluation and selection of wild specimens with desirable traits that can be used in the development of improved new cultivars. Therefore, the aim of the present paper is to review the recent progress made in the field of metabolomics and plant breeding, especially concerning the adaptive responses of legume species to abiotic stresses as well as to point out the key primary and secondary metabolites involved in the adaptation and sensing mechanisms.

A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana

Oxidative stress can lead to plant growth retardation, yield loss, and death. The atr7 mutant of Arabidopsis thaliana exhibits pronounced tolerance to oxidative stress. Using positional cloning, confirmed by knockout and RNA interference (RNAi) lines, we identified the atr7 mutation and revealed that ATR7 is a previously uncharacterized gene with orthologs in other seed plants but with no homology to genes in lower plants, fungi or animals. Expression of ATR7-GFP fusion shows that ATR7 is a nuclear-localized protein. RNA-seq analysis reveals that transcript levels of genes encoding abiotic- and oxidative stress-related transcription factors (DREB19, HSFA2, ZAT10), chromatin remodelers (CHR34), and unknown or uncharacterized proteins (AT5G59390, AT1G30170, AT1G21520) are elevated in atr7. This indicates that atr7 is primed for an upcoming oxidative stress via pathways involving genes of unknown functions. Collectively, the data reveal ATR7 as a novel seed plants-specific nuclear regulator of oxidative stress response.

Is naphthylphthalamic acid a specific phytotropin? It elevates ethylene and alters metabolic homeostasis in tomato

In higher plants, phytohormone indole-3-acetic acid is characteristically transported from the apex towards the base of the plant, termed as polar auxin transport (PAT). Among the inhibitors blocking PAT, N-1-naphthylphthalamic acid (NPA) that targets ABCB transporters is most commonly used. NPA-treated light-grown Arabidopsis seedlings show severe inhibition of hypocotyl and root elongation. In light-grown tomato seedlings, NPA inhibited root growth, but contrary to Arabidopsis stimulated hypocotyl elongation. The NPA-stimulation of hypocotyl elongation was milder in blue, red, and far-red light-grown seedlings. The NPA-treatment stimulated emission of ethylene from the seedlings. The scrubbing of ethylene by mercuric perchlorate reduced NPA-stimulated hypocotyl elongation. NPA action on hypocotyl elongation was antagonized by 1-methylcyclopropene, an inhibitor of ethylene action. NPA-treated seedlings had reduced levels of indole-3-butyric acid and higher levels of zeatin in the shoots. NPA did not alter indole-3-acetic levels in shoots. The analysis of metabolic networks indicated that NPA-treatment induced moderate shifts in the networks compared to exogenous ethylene that induced a drastic shift in metabolic networks. Our results indicate that in addition to ethylene, NPA-stimulated hypocotyl elongation in tomato may also involve zeatin and indole-3- butyric acid. Our results indicate that NPA-mediated physiological responses may vary in a species-specific fashion.

How do vascular plants perform photosynthesis in extreme environments? An integrative ecophysiological and biochemical story

In this work, we review the physiological and molecular mechanisms that allow vascular plants to perform photosynthesis in extreme environments, such as deserts, polar and alpine ecosystems. Specifically, we discuss the morpho/anatomical, photochemical and metabolic adaptive processes that enable a positive carbon balance in photosynthetic tissues under extreme temperatures and/or severe water-limiting conditions in C₃ species. Nevertheless, only a few studies have described the in situ functioning of photoprotection in plants from extreme environments, given the intrinsic difficulties of fieldwork in remote places. However, they cover a substantial geographical and functional range, which allowed us to describe some general trends. In general, photoprotection relies on the same mechanisms as those operating in the remaining plant species, ranging from enhanced morphological photoprotection to increased scavenging of oxidative products such as reactive oxygen species. Much less information is available about the main physiological and biochemical drivers of photosynthesis: stomatal conductance (g_s ), mesophyll conductance (g_m ) and carbon fixation, mostly driven by RuBisCO carboxylation. Extreme environments shape adaptations in structures, such as cell wall and membrane composition, the concentration and activation state of Calvin-Benson cycle enzymes, and RuBisCO evolution, optimizing kinetic traits to ensure functionality. Altogether, these species display a combination of rearrangements, from the whole-plant level to the molecular scale, to sustain a positive carbon balance in some of the most hostile environments on Earth.

Effects of cadmium, inorganic mercury and methyl-mercury on the physiology and metabolomic profiles of shoots of the macrophyte Elodea nuttallii

Macrophytes are known to bioaccumulate metals, but a thorough understanding of tolerance strategies and molecular impact of metals in aquatic plants is still lacking. The present study aimed to compare Hg and Cd effects in a representative macrophyte, Elodea nuttallii using physiological endpoints and metabolite profiles in shoots and cytosol. Exposure 24 h to methyl-Hg (30 ng L^-1), inorganic Hg (70 ng L^-1) and Cd (280 μg L^-1) did not affect photosynthesis, or antioxidant enzymes despite the significant accumulation of metals, confirming a sublethal stress level. In shoots, Cd resulted in a higher level of regulation of metabolites than MeHg, while MeHg resulted in the largest number of regulated metabolites and IHg treatment regulated no metabolites significantly. In cytosol, Cd regulated more metabolites than IHg and only arginine, histidine and mannose were reduced by MeHg exposure. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of data suggested that exposure to MeHg resulted in biochemical changes including aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, nitrogen metabolism, arginine and proline metabolism, cyanoamino acid metabolism, while the treatment of Cd stress caused significant variations in aminoacyl-tRNA biosynthesis and branched-chain amino acids pathways. Data supports an impact of MeHg on N homeostasis, while Cd resulted in an osmotic stress-like pattern and IHg had a low impact. Marked differences in the responses to MeHg and IHg exposure were evidenced, supporting different molecular toxicity pathways and main impact of MeHg on non-soluble compartment, while main impact of IHg was on soluble compartment. Metabolomics was used for the first time in this species and proved to be very useful to confirm and complement recent knowledge gained by transcriptomics and proteomics, highlighting the high interest of multi-omics approaches to identify early impact of environmental pollution.

Increasing phosphate inhibits cadmium uptake in plants and promotes synthesis of amino acids in grains of rice

Technologies for cleaner production of rice in cadmium (Cd) contaminated field are being explored worldwide. In order to investigate the inhibition mechanism of phosphate on Cd transport in soil-plant system, controlled experiments were performed in this study. Experimental results showed that Cd levels in roots, flag leaves, rachises and grains of rice plants (Oryza sativa L.) were significantly reduced by supplement of 0.5-2.5 g kg^-1 calcium magnesium phosphate fertilizer (CMP). Path coefficient analysis revealed that phosphorous had significant negative direct effect on Cd, but positive indirect effect on essential and non-essential amino acids. Applying 2.5 g kg^-1 CMP made the Cd concentration decreased by 45.7% while free essential and non-essential amino acids increased by 28.0-28.6% in grains. Levels of the branched-chain amino acids in grains were much higher than other essential amino acids, and increased with the amount of CMP fertilization. After application of CMP, pH of soil solution and thickness of the iron plaque around roots increased significantly. Spectra from X-ray photoelectron spectrometer (XPS) showed that content of N, P and Fe increased apparently, C, O and Ca had no change, while S decreased by 74.2% in roots after application of 2.5 g kg^-1 CMP. Meanwhile, Cd concentration in protoplasts of root cells decreased by 39.5-80.1% with the increase of CMP. These results indicate that application of CMP can effectively inhibit Cd accumulation in root protoplasts by promoting iron plaque formation on the root surface, reduce Cd concentration and increase free amino acids in rice grains.

Comparative proteomic analysis reveals that exogenous 6-benzyladenine (6-BA) improves the defense system activity of waterlogged summer maize

BACKGROUND

Exogenous 6-benzyladenine (6-BA) could improve leaf defense system activity. In order to better understand the regulation mechanism of exogenous 6-benzyladenine (6-BA) on waterlogged summer maize, three treatments including control (CK), waterlogging at the third leaf stage for 6 days (V3-6), and application of 100 mg dm- 3 6-BA after waterlogging for 6 days (V3-6-B), were employed using summer maize hybrid DengHai 605 (DH605) as the experimental material. We used a labeling liquid chromatography-based quantitative proteomics approach with tandem mass tags to determine the changes in leaf protein abundance level at the tasseling stage.

RESULTS

Waterlogging significantly hindered plant growth and decreased the activities of SOD, POD and CAT. In addition, the activity of LOX was significantly increased after waterlogging. As a result, the content of MDA and H2O2 was significantly increased which incurred serious damages on cell membrane and cellular metabolism of summer maize. And, the leaf emergence rate, plant height and grain yield were significantly decreased by waterlogging. However, application of 6-BA effectively mitigated these adverse effects induced by waterlogging. Compared with V3-6, SOD, POD and CAT activity of V3-6-B were increased by 6.9, 12.4, and 18.5%, LOX were decreased by 13.6%. As a consequence, the contents of MDA and H2O2 in V3-6-B were decreased by 22.1 and 17.2%, respectively, compared to that of V3-6. In addition, the leaf emergence rate, plant height and grain yield were significantly increased by application of 6-BA. Based on proteomics profiling, the proteins involved in protein metabolism, ROS scavenging and fatty acid metabolism were significantly regulated by 6-BA, which suggested that application of 6-BA exaggerated the defensive response of summer maize at proteomic level.

CONCLUSIONS

These results demonstrated that 6-BA had contrastive effects on waterlogged summer maize. By regulating key proteins related to ROS scavenging and fatty acid metabolism, 6-BA effectively increased the defense system activity of waterlogged summer maize, then balanced the protein metabolism and improved the plant physiological traits and grain yield.

Metabolite profiling reveals a complex response of plants to application of plant growth-promoting endophytic bacteria

Endophytic bacteria have been explored for their role in plant growth promotion, however, not much has been explored in cucumber. The metabolomic response of plants to application of such microbes also remains largely unknown. Thus, we investigated the application of endophytic bacteria to cucumber to infer their role in plant growth promotion and document metabolome response. The lowest healthy leaf-stalks were sampled from four differently sourced cucumber plants, and endophytic bacteria were isolated after surface disinfection. Initial plant growth-promoting (PGP) screening was performed to identify PGP strains out of numerous isolates, and five strains (Strains 4=Curtobacterium spp., 72=Brevibacillus spp., 167=Paenibacillus spp., 193=Bacillus spp., and 227=Microbacterium spp.) were selected based on their contribution to root growth compared with the control. The selected strains were further evaluated in pot experiments, axenic PGP trait assays, and metabolomic analysis. Results revealed that the selected isolates possessed different qualitative characteristics among indole acetic acid, siderophore production, phosphate solubilization, and 1-aminocyclopropane-1-carboxylate (ACC)-deaminase and nifH genes, and all isolates significantly enhanced plant growth in both pot experiments compared with the uninoculated control and fertilizer control. Metabolomic profiling revealed that both strains affected the plant metabolomes compared with the uninoculated control. Around 50 % of the metabolites explored had higher concentrations in either or both bacteria-applied plants compared with the uninoculated control. Differences were observed in both strains' regulation of metabolites, although both enhanced root growth near equally. Overall, endophytic bacteria significantly enhanced plant growth and tended to produce or induce release of certain metabolites within the plant endosphere.

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis

Plant-derived natural products have long been considered a valuable source of lead compounds for drug development. Natural extracts are usually composed of hundreds to thousands of metabolites, whereby the bioactivity of natural extracts can be represented by synergism between several metabolites. However, isolating every single compound from a natural extract is not always possible due to the complex chemistry and presence of most secondary metabolites at very low levels. Metabolomics has emerged in recent years as an indispensable tool for the analysis of thousands of metabolites from crude natural extracts, leading to a paradigm shift in natural products drug research. Analytical methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) are used to comprehensively annotate the constituents of plant natural products for screening, drug discovery as well as for quality control purposes such as those required for phytomedicine. In this review, the current advancements in plant sample preparation, sample measurements, and data analysis are presented alongside a few case studies of the successful applications of these processes in plant natural product drug discovery.

A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress

Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels.

Enhancing trehalose biosynthesis improves yield potential in marker-free transgenic rice under drought, saline, and sodic conditions

Edaphic factors such as salinity, sodicity, and drought adversely affect crop productivity, either alone or in combination. Despite soil sodicity being reported as an increasing problem worldwide, limited efforts have been made to address this issue. In the present study, we aimed to generate rice with tolerance to sodicity in conjunction with tolerance to salinity and drought. Using a fusion gene from E. coli coding for trehalose-6-phosphate synthase/phosphatase (TPSP) under the control of an ABA-inducible promoter, we generated marker-free, high-yielding transgenic rice (in the IR64 background) that can tolerate high pH (~9.9), high EC (~10.0 dS m-1), and severe drought (30-35% soil moisture content). The transgenic plants retained higher relative water content (RWC), chlorophyll content, K+/Na+ ratio, stomatal conductance, and photosynthetic efficiency compared to the wild-type under these stresses. Positive correlations between trehalose overproduction and high-yield parameters were observed under drought, saline, and sodic conditions. Metabolic profiling using GC-MS indicated that overproduction of trehalose in leaves differently modulated other metabolic switches, leading to significant changes in the levels of sugars, amino acids, and organic acids in transgenic plants under control and stress conditions. Our findings reveal a novel potential technological solution to tackle multiple stresses under changing climatic conditions.

Biomarkers for grain yield stability in rice under drought stress

Crop yield stability requires an attenuation of the reduction of yield losses caused by environmental stresses such as drought. Using a combination of metabolomics and high-throughput colorimetric assays, we analysed central metabolism and oxidative stress status in the flag leaf of 292 indica rice (Oryza sativa) accessions. Plants were grown in the field and were, at the reproductive stage, exposed to either well-watered or drought conditions to identify the metabolic processes associated with drought-induced grain yield loss. Photorespiration, protein degradation, and nitrogen recycling were the main processes involved in the drought-induced leaf metabolic reprogramming. Molecular markers of drought tolerance and sensitivity in terms of grain yield were identified using a multivariate model based on the values of the metabolites and enzyme activities across the population. The model highlights the central role of the ascorbate-glutathione cycle, particularly dehydroascorbate reductase, in minimizing drought-induced grain yield loss. In contrast, malondialdehyde was an accurate biomarker for grain yield loss, suggesting that drought-induced lipid peroxidation is the major constraint under these conditions. These findings highlight new breeding targets for improved rice grain yield stability under drought.

Drought and Salinity Stress Responses and Microbe-Induced Tolerance in Plants

Drought and salinity are among the most important environmental factors that hampered agricultural productivity worldwide. Both stresses can induce several morphological, physiological, biochemical, and metabolic alterations through various mechanisms, eventually influencing plant growth, development, and productivity. The responses of plants to these stress conditions are highly complex and depend on other factors, such as the species and genotype, plant age and size, the rate of progression as well as the intensity and duration of the stresses. These factors have a strong effect on plant response and define whether mitigation processes related to acclimation will occur or not. In this review, we summarize how drought and salinity extensively affect plant growth in agriculture ecosystems. In particular, we focus on the morphological, physiological, biochemical, and metabolic responses of plants to these stresses. Moreover, we discuss mechanisms underlying plant-microbe interactions that confer abiotic stress tolerance.

Functional Relevance of Citrulline in the Vegetative Tissues of Watermelon During Abiotic Stresses

A non-protein amino acid, citrulline, is a compatible solute involved in the maintenance of cellular osmolarity during abiotic stresses. Despite its significance, a coherent model indicating the role of citrulline during stress conditions has not yet emerged. We have used watermelon, naturally rich in citrulline, as a model to understand its accumulation during drought stress and nitrogen perturbation using transcriptomic and metabolomic analysis. Experiments were performed in the semi-controlled environment, and open field to study the accumulation of drought-induced citrulline in the vegetative tissues of watermelon by monitoring the stress treatments using physiological measurements. The amino acid profiling of leaves and stems in response to drought stress showed up to a 38 and 16-fold increase in citrulline content, respectively. Correlation between amino acids indicated a concomitant activation of a metabolic pathway that included citrulline, its precursor (ornithine), and catabolic product (arginine). Consistent with its accumulation, the gene expression analysis and RNA-Sequencing confirmed activation of citrulline biosynthesis-related genes - Ornithine carbamoyl-transferase (OTC), N-acetylornithine deacetylase (AOD) and Carbamoyl phosphate synthases (CPS), and down-regulation of catabolic genes; Arginosuccinate lyase (ASL) and Arginosuccinate synthases (ASS) in drought-stressed leaf tissues. Based on the relative abundance in the nitrogen-depleted vegetative tissues and down-regulation of genes involved in citrulline biosynthesis, we also demonstrated that the nitrogen status of the plant regulates citrulline. Taken together, these data provide further insights into the metabolic and molecular mechanisms underlying the amino acid metabolism under environmental stress and the significance of non-protein amino acid citrulline in plants.

Drought Stress Responses and Resistance in Plants: From Cellular Responses to Long-Distance Intercellular Communication

The drought stress responses of vascular plants are complex regulatory mechanisms because they include various physiological responses from signal perception under water deficit conditions to the acquisition of drought stress resistance at the whole-plant level. It is thought that plants first recognize water deficit conditions in roots and that several molecular signals then move from roots to shoots. Finally, a phytohormone, abscisic acid (ABA) is synthesized mainly in leaves. However, the detailed molecular mechanisms of stress sensors and the regulators that initiate ABA biosynthesis in response to drought stress conditions are still unclear. Another important issue is how plants adjust ABA propagation, stress-mediated gene expression and metabolite composition to acquire drought stress resistance in different tissues throughout the whole plant. In this review, we summarize recent advances in research on drought stress responses, focusing on long-distance signaling from roots to shoots, ABA synthesis and transport, and metabolic regulation in both cellular and whole-plant levels of Arabidopsis and crops. We also discuss coordinated mechanisms for acquiring drought stress adaptations and resistance via tissue-to-tissue communication and long-distance signaling.

Foliar spray of TiO2 nanoparticles prevails over root application in reducing Cd accumulation and mitigating Cd-induced phytotoxicity in maize (Zea mays L.)

Cadmium (Cd) pollution is considered one of the global environmental issues due to its adverse effects on plant and human health. With the rapid development of nanotechnology and the practical application of engineered nanoparticles (ENPs) in agriculture, the mechanisms underlying the interactions between NPs and heavy metal on their uptake, accumulation, and phytotoxicity in crops are still not fully understood. Therefore, the impact of TiO₂ NPs (0, 100, 250 mg/L) and Cd (0, 50 μM) co-exposure on hydroponic maize (Zea mays L.) was determined under two exposure modes. Results showed that root co-exposure to TiO₂ NPs and 100 mg/L Cd significantly enhanced Cd uptake and produced greater phytotoxicity in maize than foliar exposure to TiO₂ NPs. Meanwhile, plant dry weight and chlorophyll content showed a reduction of 45.3% and 50.5%, respectively, when compared with single Cd treatment. In addition, the accumulation of Ti in shoots and roots increased by 1.61 and 4.29 times, respectively when root exposure to 250 mg/L TiO₂ NPs. By contrast, foliar exposure of TiO₂ NPs could markedly decrease shoot Cd contents from 15.2% to 17.8% and had a stronger influence on alleviating Cd-induced toxicity via increasing superoxide dismutase (SOD) and glutathione S-transferase (GST) activities and upregulating several metabolic pathways, including galactose metabolism and citrate cycle, alanine, aspartate and glutamate metabolism, as well as glycine, serine and threonine metabolism. This study provides a new strategy for the application of TiO₂ NPs in crop safety production in Cd contaminated soils.

PGDH family genes differentially affect Arabidopsis tolerance to salt stress

The first step in the Phosphorylated Pathway of serine (Ser) Biosynthesis (PPSB) is catalyzed by the enzyme Phosphoglycerate Dehydrogenase (PGDH), coded in Arabidopsis thaliana by three genes. Gene expression analysis indicated that PGDH1 and PGDH2 were induced, while PGDH3 was repressed, by salt-stress. Accordingly, PGDH3 overexpressing plants (Oex PGDH3) were more sensitive to salinity than wild type plants (WT), while plants overexpressing PGDH1 (Oex PGDH1) performed better than WT under salinity conditions. Oex PGDH1 lines displayed lower levels of the salt-stress markers proline and raffinose in roots than WT under salt-stress conditions. Besides, the ratio of oxidized glutathione (GSSG) without and with salt-stress was the highest in Oex PGDH1, and the lowest in Oex PGDH3 compared to WT. These results corroborated that PGDH3 activity could be detrimental, while PGDH1 activity could be beneficial for plant salt tolerance. Under salt-stress conditions, PGDH1 overexpression increased Ser content only in roots, while PGDH3 overexpression increased the amino acid level in both aerial parts and roots, compared to the WT. Our results indicate that the response of PGDH family genes to salt-stress depends on the specific gene studied and that increases in Ser content are not always correlated with enhanced plant salt tolerance.

Can Metabolite- and Transcript-Based Selection for Drought Tolerance in Solanum tuberosum Replace Selection on Yield in Arid Environments?

Climate models predict an increased likelihood of drought, demanding efficient selection for drought tolerance to maintain yield stability. Classic tolerance breeding relies on selection for yield in arid environments, which depends on yield trials and takes decades. Breeding could be accelerated by marker-assisted selection (MAS). As an alternative to genomic markers, transcript and metabolite markers have been suggested for important crops but also for orphan corps. For potato, we suggested a random-forest-based model that predicts tolerance from leaf metabolite and transcript levels with a precision of more than 90% independent of the agro-environment. To find out how the model based selection compares to yield-based selection in arid environments, we applied this approach to a population of 200 tetraploid Solanum tuberosum ssp. tuberosum lines segregating for drought tolerance. Twenty-four lines were selected into a phenotypic subpopulation (PP_t) for superior tolerance based on relative tuber starch yield data from three drought stress trials. Two subpopulations with superior (MP_t) and inferior (MP_s) tolerance were selected based on drought tolerance predictions based on leaf metabolite and transcript levels from two sites. The 60 selected lines were phenotyped for yield and drought tolerance in 10 multi-environment drought stress trials representing typical Central European drought scenarios. Neither selection affected development or yield potential. Lines with superior drought tolerance and high yields under stress were over-represented in both populations selected for superior tolerance, with a higher number in PP_t compared to MP_t. However, selection based on leaf metabolites may still be an alternative to yield-based selection in arid environments as it works on leaves sampled in breeder's fields independent of drought trials. As the selection against low tolerance was ineffective, the method is best used in combination with tools that select against sensitive genotypes. Thus, metabolic and transcript marker-based selection for drought tolerance is a viable alternative to the selection on yield in arid environments.

Cytochrome respiration pathway and sulphur metabolism sustain stress tolerance to low temperature in the Antarctic species Colobanthus quitensis

Understanding the strategies employed by plant species that live in extreme environments offers the possibility to discover stress tolerance mechanisms. We studied the physiological, antioxidant and metabolic responses to three temperature conditions (4, 15, and 23°C) of Colobanthus quitensis (CQ), one of the only two native vascular species in Antarctica. We also employed Dianthus chinensis (DC), to assess the effects of the treatments in a non-Antarctic species from the same family. Using fused LASSO modelling, we associated physiological and biochemical antioxidant responses with primary metabolism. This approach allowed us to highlight the metabolic pathways driving the response specific to CQ. Low temperature imposed dramatic reductions in photosynthesis (up to 88%) but not in respiration (sustaining rates of 3.0-4.2 μmol CO₂  m^-2  s^-1 ) in CQ, and no change in the physiological stress parameters was found. Its notable antioxidant capacity and mitochondrial cytochrome respiratory activity (20 and two times higher than DC, respectively), which ensure ATP production even at low temperature, was significantly associated with sulphur-containing metabolites and polyamines. Our findings potentially open new biotechnological opportunities regarding the role of antioxidant compounds and respiratory mechanisms associated with sulphur metabolism in stress tolerance strategies to low temperature.

Phenotypic Markers Reflecting the Status of Overstressed Tea Plants Subjected to Repeated Shade Cultivation

Shade cultivation is a traditional Japanese tea cultivation method in which the shoot buds are shaded for several weeks. This technique is increasingly used for green tea production because it produces tea of high quality (as indicated by umami and nutritional content) and commands high prices. However, given that shaded tea plants are grown under low-light stress, concerns exist regarding damage to tea plants caused by repeated shade cultivation. To understand basic physiological responses and accumulative changes in photosynthetic ability and metabolites of tea plants subjected to repeated shading, we performed a pot experiment on immature tea plants grown in a growth chamber subjected to repeated shading treatments. The results demonstrated that shade cultivation caused a decrease in non-structural carbohydrate content and an increase of several degrees in leaf surface temperature, reflecting transpiration through the leaf stomata, as a result of a reduction in photosynthetic ability. An increase of several degrees in canopy temperature and a reduction in photosynthetic ability in the field in the mid-summer season was also observed in overstressed tea plants subjected to repeated shading. Metabolomic analysis identified several candidate biomarkers, such as citrulline and glycine betaine, that were significantly changed in individuals affected by shade cultivation. These physiological changes may be an indicator of the stress status of tea plants grown under repeated shade cultivation.

Insights into the metabolic responses of two contrasting Tibetan hulless barley genotypes under low nitrogen stress

Nitrogen (N) is an essential macronutrient for plants. However, excessive use of N fertilizer for cultivation is an environmental hazard. A good adaption to N deficiency is known in the Tibetan hulless barley. Therefore, it is of interest to complete the metabolic analysis on LSZQK which is a low nitrogen (low-N) sensitive genotype and Z0284 that is tolerant to low-N. We identified and quantified 750 diverse metabolites in this analysis. The two genotypes show differences in their basal metabolome under normal N condition. Polyphenols and lipids related metabolites were significantly enriched in Z0284 having a basal role prior to exposure to low-N stress. Analysis of the differentially accumulated metabolites (DAM) induced by low-N explain the genotype-specific responses. Fourteen DAMs showed similar patterns of change between low-N and control conditions in both genotypes. This could be the core low-N responsive metabolites regardless of the tolerance level in hulless barley. We also identified 4 DAMs (serotonin, MAG (18:4) isomer 2, tricin 7-O-feruloylhexoside and gluconic acid) shared by both genotypes displaying opposite patterns of regulation under low-N conditions and may play important roles in low-N tolerance. This report provides a theoretical basis for further understanding of the molecular mechanisms of low-N stress tolerance in hulless barley.

Flowers and climate change: a metabolic perspective

Adverse climatic conditions at the time of flowering severely hinder crop yields and threaten the interactions between plants and their pollinators. These features depend on a common trait: the metabolism of flowers. In this Viewpoint article, we aim to provide insight into the metabolic changes that occur in flowers in response to changes in climate and emphasize that these changes severely impact the fitness of autogamous and allogamous species, plant-pollinator interactions, and overall ecosystem health. We review the biochemical processes that lead to failure of gamete development and to alterations of color, scent and nectar secretion. Then, making use of open access expression data, we examine the expression of genes that may drive these changes in response to heat and drought. Finally, we present measurements of metabolites from flowers exposed to a heat wave and discuss how the results of this short-term experiment may give rise to misleading conclusions regarding the positive effect of heat on flower fitness. We hope this article draws attention to this often-neglected dynamic and its important consequences.

Physiological plasticity to high temperature stress in chickpea: Adaptive responses and variable tolerance

High temperature stress (HTS) is one of the most crucial factors that limits plant growth and development, and reduces crop yields worldwide. Cool-season crops, particularly the legumes, are severely affected by increasing ambient temperature associated with global climate change. We characterized the HTS-induced modulations of morpho-physicochemical traits and gene expression of several chickpea genotypes and the metabolic profile of the tolerant cultivar. Higher water use efficiency and photosynthetic capacity, minimal membrane lipid peroxidation in conjunction with increased abundance of osmolytes and secondary metabolites depicted thermotolerance of ICC 1205. The adaptive responses were accompanied by high transcript abundance of heat shock proteins and antioxidant enzymes. To integrate stress-responsive signalling and metabolic networks, the HTS-induced physicochemical analysis was further extended to metabolite profiling of the thermotolerant cultivar. The screening of the metabolome landscape led to the identification of 49 HTS-responsive metabolites that include polycarboxylic acid, sugar acids, sugar alcohols and amino acids which might confer thermotolerance in chickpea. The present study, to our knowledge, is the most comprehensive of its kind in dissecting cultivar-specific differential adaptive responses to HTS in chickpea, which might potentiate the identification of genetic traits extendible to improvement of thermotolerance of crops.

Jasmonates-Mediated Rewiring of Central Metabolism Regulates Adaptive Responses

The lipid-derived hormones jasmonates (JAs) play key functions in a wide range of physiological and developmental processes that regulate growth, secondary metabolism and defense against biotic and abiotic stresses. In this connection, biosynthesis, tissue-specific distribution, metabolism, perception, signaling of JAs have been the target of extensive studies. In recent years, the involvement of JAs signaling pathway in the regulation of growth and adaptive responses to environmental challenges has been further examined. However, JAs-mediated mechanisms underlying the transition from 'growth mode' to 'adaptive mode' remain ambiguous. Combined analysis of transgenic lines deficient in JAs signaling in conjunction with the data from JAs-treated plants revealed the function of these hormones in rewiring of central metabolism. The collective data illustrate JAs-mediated decrease in the levels of metabolites associated with active growth such as sucrose, raffinose, orotate, citrate, malate, and an increase in phosphorylated hexoses, responsible for the suppression of growth and photosynthesis, concurrent with the induction of protective metabolites, such as aromatic and branched-chain amino acids, and aspartate family of metabolites. This finding provides an insight into the function of JAs in shifting the central metabolism from the production of growth-promoting metabolites to protective compounds and expands our understanding of the role of JAs in resource allocation in response to environmental challenges.

Metabolomics and transcriptomics reveal defense mechanism of rice (Oryza sativa) grains under stress of 2,2',4,4'-tetrabromodiphenyl ether

2,2',4,4'-Tetrabromodiphenyl ether (BDE-47), a predominant polybrominated diphenyl ether (PBDE), has received extensive attention for its potential environmental impact. An integrated study of metabolomics and transcriptomics was conducted on two rice (Oryza sativa) cultivars, Lianjing-7 (LJ-7) and Yongyou-9 (YY-9), which have been identified as tolerant and sensitive cultivars to BDE-47, respectively. The objective was to investigate the molecular mechanisms of their different ability to tolerate BDE-47. Both rice plants were cultivated to maturity in soils containing three concentrations of BDE-47 (10, 20, and 50 mg/kg). Metabolomic analyses of rice grains identified 65 metabolites in LJ-7 and 45 metabolites in YY-9, including amino acids, saccharides, organic acids, fatty acids, and secondary metabolites. In the tolerant cultivar LJ-7 exposed to 50 mg/kg BDE-47, concentrations of most of the metabolites increased significantly, with α-ketoglutaric acid increased by 20-fold and stigmastanol increased by 12-fold. In the sensitive cultivar YY-9, the concentrations of most metabolites increased after the plant was exposed to 1 and 10 mg/kg BDE-47 but decreased after the plant was exposed to 50 mg/kg BDE-47. Transcriptomic data demonstrated that regulation of gene expressions was affected most in LJ-7 exposed to 50 mg/kg BDE-47 (966 genes up-regulated and 620 genes down-regulated) and in YY-9 exposed to 10 mg/kg BDE-47 (85 genes up-regulated and 291 genes down-regulated), in good accordance with the observed metabolic alternation in the two cultivars. Analyses of metabolic pathways and KEGG enrichment revealed that many biological processes, including energy consumption and biosynthesis, were perturbed in the two rice cultivars by BDE-47. A majority of metabolites and genes involved in dominating pathways of energy consumption (e.g., tricarboxylic acid cycle) and the biosynthesis (e.g., metabolism of saccharides and amino acids) were enhanced in LJ-7 by BDE-47. In contrast, energy consumption was increased while biosynthetic processes were inhibited in YY-9 by BDE-47, which could lead to the sensitivity of YY-9 to BDE-47. The combined results suggest that the different defensive abilities of these two rice cultivars in response to BDE-47 could be attributed to their differences in energy-consumption strategy and biosynthesis of nutritional components in grains. This study provides a useful reference for rice cultivation in PBDE-polluted areas.

Site-dependent induction of jasmonic acid-associated chemical defenses against western flower thrips in Chrysanthemum

Local and systemic induction of JA-associated chemical defenses and resistance to western flower thrips in Chrysanthemum are spatially variable and dependent on the site of the JA application. Plants have evolved numerous inducible defense traits to resist or tolerate herbivory, which can be activated locally at the site of the damage, or systemically through the whole plant. Here we investigated how activation of local and systemic chemical responses upon exogenous application of the phytohormone jasmonic acid (JA) varies along the plant canopy in Chrysanthemum, and how these responses correlate with resistance to thrips. Our results showed that JA application reduced thrips damage per plant when applied to all the plant leaves or when locally applied to apical leaves, but not when only basal leaves were locally treated. Local application of JA to apical leaves resulted in a strong reduction in thrips damage in new leaves developed after the JA application. Yet, activation of a JA-associated defensive protein marker, polyphenol oxidase, was only locally induced. Untargeted metabolomic analysis further showed that JA increased the concentrations of sugars, phenylpropanoids, flavonoids and some amino acids in locally induced basal and apical leaves. However, local application of JA to basal leaves marginally affected the metabolomic profiles of systemic non-treated apical leaves, and vice versa. Our results suggest that JA-mediated activation of systemic chemical defense responses is spatially variable and depends on the site of the application of the hormone in Chrysanthemum.

Sorting the Wheat From the Chaff: Programmed Cell Death as a Marker of Stress Tolerance in Agriculturally Important Cereals

Conventional methods for screening for stress-tolerant cereal varieties rely on expensive, labour-intensive field testing and molecular biology techniques. Here, we use the root hair assay (RHA) as a rapid screening tool to identify stress-tolerant varieties at the early seedling stage. Wheat and barley seedlings had stress applied, and the response quantified in terms of programmed cell death (PCD), viability and necrosis. Heat shock experiments of seven barley varieties showed that winter and spring barley varieties could be partitioned into their two distinct seasonal groups based on their PCD susceptibility, allowing quick data-driven evaluation of their thermotolerance at an early seedling stage. In addition, evaluating the response of eight wheat varieties to heat and salt stress allowed identification of their PCD inflection points (35°C and 150 mM NaCl), where the largest differences in PCD levels arise. Using the PCD inflection points as a reference, we compared different stress effects and found that heat-susceptible wheat varieties displayed similar vulnerabilities to salt stress. Stress-induced PCD levels also facilitated the assessment of the basal, induced and cross-stress tolerance of wheat varieties using single, combined and multiple individual stress exposures by applying concurrent heat and salt stress in a time-course experiment. Two stress-susceptible varieties were found to have low constitutive resistance as illustrated by their high PCD levels in response to single and combined stress exposure. However, both varieties had a fast, adaptive response as PCD levels declined at the other time-points, showing that even with low constitutive resistance, the initial stress cue primes cross-stress tolerance adaptations for enhanced resistance even to a second, different stress type. Here, we demonstrate the RHA's suitability for high-throughput analysis (∼4 days from germination to data collection) of multiple cereal varieties and stress treatments. We also showed the versatility of using stress-induced PCD levels to investigate the role of constitutive and adaptive resistance by exploring the temporal progression of cross-stress tolerance. Our results show that by identifying suboptimal PCD levels in vivo in a laboratory setting, we can preliminarily identify stress-susceptible cereal varieties and this information can guide further, more efficiently targeted, field-scale experimental testing.

Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses

Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce their long-term evolutionary potential. However, appropriate short-term plastic responses to new environmental conditions might not require high levels of standing genetic variation. In this study, we tested whether mating system variation among populations, and associated changes in genetic variability, affected short-term responses to environmental challenges. We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a perennial plant, Arabidopsis lyrata, under constant growth chamber conditions and an outdoor common garden environment outside its native range. We found no effect of inbreeding on survival, flowering phenology or short-term physiological responses. Specifically, naturally occurring inbreeding had no significant effects on the plasticity of metabolome profiles, using either multivariate approaches or analysis of variation in individual metabolites, with inbreeding populations showing similar physiological responses to outbreeding populations over time in both growing environments. We conclude that low genetic diversity in naturally inbred populations may not always compromise fitness or short-term physiological capacity to respond to environmental change, which could help to explain the global success of selfing mating strategies.

Comparative molecular and metabolic responses of wheat seedlings (Triticum aestivum L.) to the imazethapyr enantiomers S-IM and R-IM

The enantioselective effects of imazethapyr (IM) enantiomers on wheat seedlings in a hydroponic medium were studied. R-IM at 0.05mg/L exerted a stronger inhibitory effect on shoot weight and root weight than 0.05mg/L S-IM, suggesting that R-IM more severely inhibited growth. Oxidative damage, based on the anthocyanin content, malondialdehyde (MDA) content, antioxidant enzyme activities and transcript levels of antioxidant enzyme genes, were studied together with the cellular ultrastructure of wheat leaves. The anthocyanin and MDA contents in the R-IM treatment group were significantly increased compared with those in the control group, but no significant changes were observed in the S-IM treatment group. The antioxidant enzyme activities of CAT and SOD were inhibited by 0.32- and 0.73-fold, respectively, in the 14day R-IM treatment group compared to those in the control. However, the transcript levels of antioxidant enzyme genes, including CuZnSOD, POD and CAT, were downregulated in the 14day R-IM exposure group, but those of DHAR were not. The number and size of starch granules increased and chloroplast swelling was observed in wheat leaf cells after R-IM exposure, which showed that photosynthetic functions were potentially disturbed. These results directly or indirectly imply that R-IM exposure causes more oxidative stress and exerts a stronger negative effect on wheat than S-IM. A metabolomics approach revealed that the tricarboxylic acid cycle was heavily suppressed by R-IM treatment. Some amino acids (proline, threonine, lysine, valine) were increased by only the R-IM treatment, indicating the activation of antioxidant pathways. The decrease in a series of fatty acids implied that the cell membrane composition changed in response to R-IM. These results provide a deeper understanding of the enantioselective effects of IM enantiomers on the molecular and metabolic responses in wheat seedlings.

The Power of Electropenetrography in Enhancing Our Understanding of Host Plant-Vector Interactions

The invasive Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae), is the primary vector of the phloem-infecting bacterium, Candidatus Liberibacter asiaticus. Candidatus L. asiaticus is the putative causal agent of Huanglongbing (HLB) disease, a destructive disease of Citrus. While many Citrus species are susceptible to D. citri probing and HLB disease, there are marked behavioral differences in D. citri probing responses and Ca. Liberibacter asiaticus infection severity among Citrus species. Using four mandarin hybrid selections and pummelo plants variably resistant to D. citri probing, oviposition, and survival, we explored probing differences using electropenetrography (EPG), conducted an oviposition and survival study, and determined host plant metabolites using gas-chromatography mass-spectroscopy (GC-MS). We found thirty-seven D. citri probing variables to be significantly different among tested mandarin selections and pummelo, in addition to differential oviposition and survivorship abilities on tested plants. We found sixty-three leaf metabolites with eight being significantly different among tested mandarin selections and pummelo. Detailed analysis of probing behavior, oviposition, survivorship, and host plant metabolite concentrations reveals the complex, layered resistance mechanisms utilized by resistant Citrus against D. citri probing. EPG is a powerful technology for screening Asian citrus psyllid resistant Citrus to elucidate host plant-vector interactions, with an aim to minimize vector probing and eliminate the spread of the bacterial pathogen, Ca. L. asiaticus.

Metabolomics characterizes metabolic changes of Apocyni Veneti Folium in response to salt stress

Apocyni Veneti Folium (AVF) has been raised great interest in the antioxidant properties recently for the preservation of human health. However, little research was found on the integrate metabolites except our previous investigation on the variations of the bioactive constituents. To understand the salt-tolerant mechanisms of the halophyte, metabolomic platform based on ultra-fast liquid chromatography tandem triple time-of-flight mass/mass spectrometer was applied in this study. The results showed that metabolic profiles were separated and differentiated among groups based on multivariate statistical analysis; different metabolites belonged to various chemical classes. Besides, phenylpropanoid pathway and terpenoid biosynthesis were disturbed in all salt-stressed AVF and low salt-treated group appeared to be better than other samples in terms of relative contents (peak areas) of the wide variety of bioactive components and physiological variations of photosynthetic pigments, osmotic homeostasis, lipid peroxidation product and antioxidative enzymes. This study may provide additional insight into the salt-tolerant mechanisms and the quality assessment of AVF in a holistic level based on the plant metabolomics.

Adaptation of the metabolomics profile of rice after Pyricularia oryzae infection

Pyricularia oryzae (P. oryzae), one of the most devastating fungal pathogens, is the cause of blast disease in rice. Infection with a blast fungus induces biological responses in the host plant that lead to its survival through the termination or suppression of pathogen growth, and metabolite compounds play vital roles in plant interactions with a wide variety of other organisms. Numerous studies have indicated that rice has a multi-layered plant immune system that includes pre-developed (e.g., cell wall and phytoanticipins), constitutive and inducible (phytoalexins) defence barriers against stresses. Significant progress towards understanding the basis of the molecular mechanisms underlying the defence responses of rice to P. oryzae has been achieved. Nonetheless, even though the important metabolites in the responses of rice to pathogens have been identified, their exact mechanisms and their contributions to plant immunity against blast fungi have not been elucidated. The purpose of this review is to summarize and discuss recent advances towards the understanding of the integrated metabolite variations in rice after P. oryzae invasion.

Insights into physiological responses of mosses Physcomitrella patens and Pohlia drummondii to lichen secondary metabolites

It is widely accepted that allelopathy among mosses and lichens do exist due to its similar ecological needs, though it is rarely documented. With an aim to test whether there is an effect of allelochemicals to mosses, we grow axenically two moss species (namely Physcomitrella patens and Pohlia drummondii) in controlled conditions and use them to test the effect of lichen Pseudevernia furfuracea acetone extracts containing active compounds: atranorin, chloratranorin, and physodic acid. The photosynthesis value and the biochemical parameters were measured to detect changes in moss organisms upon application of different concentration of lichen extract. The results obtained clearly showed that both moss species reacted to allelochemicals applied in test but to different extent. This suggests that tested moss species have various patterns on reaction to allelochemicals, and that the process of allelopathy is rather a recently coevolving one, than pre-defined. The lichen secondary metabolites are allelochemicals effective also to moss species that are not selected lichen cohabitants.

Competing Endogenous RNA Networks Underlying Anatomical and Physiological Characteristics of Poplar Wood in Acclimation to Low Nitrogen Availability

Although poplar plantations are often established on nitrogen (N)-poor soil, the physiological and molecular mechanisms underlying wood properties of poplars in acclimation to low N availability remain largely unknown. To investigate wood properties of poplars in acclimation to low N, Populus � canescens saplings were exposed to either 50 (low N) or 500 (normal N) �M NH4NO3 for 2 months. Low N resulted in decreased xylem width and cell layers of the xylem (the number of cells counted along the ray parenchyma on the stem cross section), narrower lumina of vessels and fibers, greater thickness of double fiber walls (the walls between two adjacent fiber cells), more hemicellulose and lignin deposition, and reduced cellulose accumulation in poplar wood. Consistently, concentrations of gibberellins involved in cell size determination and the abundance of various metabolites including amino acids, carbohydrates and precursors for cell wall biosynthesis were decreased in low N-supplied wood. In line with these anatomical and physiological changes, a number of mRNAs, long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) were significantly differentially expressed. Competing endogenous RNA regulatory networks were identified in the wood of low N-treated poplars. Overall, these results indicate that miRNAs-lncRNAs-mRNAs networks are involved in regulating wood properties and physiological processes of poplars in acclimation to low N availability.

A metabolomic strategy revealed the role of JA and SA balance in Clematis terniflora DC. Response to UVB radiation and dark

Clematis terniflora DC. is a valuable resource with potential high pharmaceutical value. Proteomic, transcriptomic and metabolomic analyses of C. terniflora that has been exposed to high levels of UVB irradiation and dark conditions (HUVB + D) have revealed the mechanisms underlying its medicinal potential. However, the signal transduction pathways and the mechanisms of regulation for the accumulation of secondary metabolites remain unclear. In this study, we show that the jasmonic acid (JA) and salicylic acid (SA) signals were activated in C. terniflora in response to HUVB + D. Metabolomic analysis demonstrated that the perturbation in JA and SA balance led to additional reallocation of carbon and nitrogen resources. Evaluating the fold change ratios of differentially changed metabolites proved that JA signal enhanced the transformation of nitrogen to carbon through the 4-aminobutyric acid (GABA) shunt pathway, which increased the carbon reserve to be utilized in the production of secondary metabolites. However, SA signal induced the synthesis of proline, while avoiding the accumulation of secondary metabolites. Over all, the results indicate that the co-increase of JA and SA reconstructed the dynamic stability of transformation from nitrogen to carbon, which effectively enhanced the oxidative defense to HUVB + D in C. terniflora by increasing the secondary metabolites.

Temperature alters susceptibility of Picea abies seedlings to airborne pollutants: The case of CdO nanoparticles

Although plants are often exposed to atmospheric nanoparticles (NPs), the mechanism of NP deposition and their effects on physiology and metabolism, and particularly in combination with other stressors, are not yet understood. Exploring interactions between stressors is particularly important for understanding plant responses in urban environments where elevated temperatures can be associated with air pollution. Accordingly, 3-year-old spruce seedlings were exposed for 2 weeks to aerial cadmium oxide (CdO) NPs of environmentally relevant size (8-62 nm) and concentration (2 × 10⁵ cm^-3). While half the seedlings were initially acclimated to high temperature (35 °C) and vapour pressure deficit (VPD; 2.81 kPa), the second half of the plants were left under non-stressed conditions (20 °C, 0.58 kPa). Atomic absorption spectrometry was used to determine Cd content in needles, while gas and liquid chromatography was used to determine changes in primary and secondary metabolites. Photosynthesis-related processes were explored with gas-exchange and chlorophyll fluorescence systems. Our work supports the hypothesis that atmospheric CdO NPs penetrate into leaves but high temperature and VPD reduce such penetration due to stomatal closure. The hypothesis that atmospheric CdO NPs influences physiological and metabolic processes in plants was also confirmed. This impact strengthens with increasing time of exposure. Finally, we found evidence that plants acclimated to stress conditions have different sensitivity to CdO NPs compared to plants not so acclimated. These findings have important consequences for understanding impacts of global warming on plants and indicates that although the effects of elevated temperatures can be deleterious, this may limit other forms of plant stress associated with air pollution.

Wheat drought tolerance in the field is predicted by amino acid responses to glasshouse-imposed drought

Water limits crop productivity, so selecting for a minimal yield gap in drier environments is critical to mitigate against climate change and land-use pressure. We investigated the responses of relative water content (RWC), stomatal conductance, chlorophyll content, and metabolites in flag leaves of commercial wheat (Triticum aestivum L.) cultivars to three drought treatments in the glasshouse and in field environments. We observed strong genetic associations between glasshouse-based RWC, metabolites, and yield gap-based drought tolerance (YDT; the ratio of yield in water-limited versus well-watered conditions) across 18 field environments spanning sites and seasons. Critically, RWC response to glasshouse drought was strongly associated with both YDT (r2=0.85, P<8E-6) and RWC under field drought (r2=0.77, P<0.05). Moreover, multiple regression analyses revealed that 98% of genetic YDT variance was explained by drought responses of four metabolites: serine, asparagine, methionine, and lysine (R2=0.98; P<0.01). Fitted coefficients suggested that, for given levels of serine and asparagine, stronger methionine and lysine accumulation was associated with higher YDT. Collectively, our results demonstrate that high-throughput, targeted metabolic phenotyping of glasshouse-grown plants may be an effective tool for selection of wheat cultivars with high field-derived YDT.

Dynamics of Short-Term Metabolic Profiling in Radish Sprouts (Raphanus sativus L.) in Response to Nitrogen Deficiency

Nitrogen (N) is a macronutrient important for the survival of plants. To investigate the effects of N deficiency, a time-course metabolic profiling of radish sprouts was performed. A total of 81 metabolites—including organic acids, inorganic acid, amino acids, sugars, sugar alcohols, amines, amide, sugar phosphates, policosanols, tocopherols, phytosterols, carotenoids, chlorophylls, and glucosinolates—were characterized. Principal component analysis and heat map showed distinction between samples grown under different N conditions, as well as with time. Using PathVisio, metabolic shift in biosynthetic pathways was visualized using the metabolite data obtained for 7 days. The amino acids associated with glucosinolates accumulated as an immediate response against –N condition. The synthesis of pigments and glucosinolates was decreased, but monosaccharides and γ-tocopherol were increased as antioxidants in radish sprouts grown in –N condition. These results indicate that in radish sprouts, response to N deficiency occurred quickly and dynamically. Thus, this metabolic phenotype reveals that radish responds quickly to N deficiency by increasing the content of soluble sugars and γ-tocopherol, which acts as a defense mechanism after the germination of radish seeds.

Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species

BACKGROUND

Suaeda salsa L. (S. salsa) is an annual euhalophyte with high salt tolerance and high value as an oil crop, traditional Chinese medicine and vegetable. However, there are few comprehensive studies on the metabolomics of S. salsa under saline conditions.

RESULTS

Seedlings of S. salsa were cultured with 0, 200 and 500 mM NaCl for two days. Then, widely targeted metabolites were detected with ultra performance liquid chromatography and tandem mass spectrometry. A total of 639 metabolites were annotated. Among these, 253 metabolites were differential metabolites. Salt treatment increased the content of certain metabolites, such as nucleotide and its derivates, organic acids, the content of amino acids, lipids such as α-linolenic acid, and certain antioxidants such as quercetin. These substances may be correlated to osmotic tolerance, increased antioxidant activity, and medical and nutritional value in the species.

CONCLUSION

This study comprehensively analyzed the metabolic response of S. salsa under salinity from the perspective of omics, and provides an important theoretical basis for understanding salt tolerance and evaluating nutritional value in the species.

Enhancement of co-production of nutritional protein and carotenoids in Dunaliella salina using a two-phase cultivation assisted by nitrogen level and light intensity

Microalga Dunaliella salina is known for its carotenogenesis. At the same time, it can also produce high-quality protein. The optimal conditions for D. salina to co-produce intracellular pools of both compounds, however, are yet unknown. This study investigated a two-phase cultivation strategy to optimize combined high-quality protein and carotenoid production of D. salina. In phase-one, a gradient of nitrogen concentrations was tested. In phase-two, effects of nitrogen pulse and high illumination were tested. Results reveal optimized protein quantity, quality (expressed as essential amino acid index EAAI) and carotenoids content in a two-phase cultivation, where short nitrogen starvation in phase-one was followed by high illumination during phase-two. Adopting this strategy, productivities of protein, EAA and carotenoids reached 22, 7 and 3 mg/L/d, respectively, with an EAAI of 1.1. The quality of this biomass surpasses FAO/WHO standard for human nutrition, and the observed level of β-carotene presents high antioxidant pro-vitamin A activity.